This repo has been deprecated. See tiramisu-brulee for a maintained version.
PyTorch-based deep neural network for multiple sclerosis lesion segmentation; specifically, T2 lesions in the brain.
This package was developed by Jacob Reinhold and the other students and researchers of the Image Analysis and Communication Lab (IACL).
- nibabel >= 3.1
- numpy >= 1.18
- pytorch >= 1.5
- pytorch_lightning >= 0.8.4
- torchio >= 0.17
From inside this directory, run:
python setup.py install
or (if you'd like to make updates to the package)
python setup.py develop
Unit tests can be run from the main directory as follows:
nosetests -v tests
[1] Zhang, Huahong, et al. "Multiple sclerosis lesion segmentation with Tiramisu and 2.5D stacked slices." International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Cham, 2019.